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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4653 | |||||||||
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Title | Packaging of DNA Origami in Viral Capsids | |||||||||
![]() | Masked SV40 capsid, encapsulating DNA origami. | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 Å | |||||||||
![]() | Kopatz I / Zalk R / Levi-Kalisman Y / Zlotkin-Rivkin E / Frank GA / Kler S | |||||||||
![]() | ![]() Title: Packaging of DNA origami in viral capsids. Authors: Idit Kopatz / Ran Zalk / Yael Levi-Kalisman / Efrat Zlotkin-Rivkin / Gabriel A Frank / Stanislav Kler / ![]() Abstract: Here we show the encapsulation of 35 nm diameter, nearly-spherical, DNA origami by self-assembly of SV40-like (simian virus 40) particles. The self-assembly of this new type of nanoparticles is ...Here we show the encapsulation of 35 nm diameter, nearly-spherical, DNA origami by self-assembly of SV40-like (simian virus 40) particles. The self-assembly of this new type of nanoparticles is highly reproducible and efficient. The structure of these particles was determined by cryo-EM. The capsid forms a regular SV40 lattice of T = 7d icosahedral symmetry and the structural features of encapsulated DNA origami are fully visible. These particles are a promising biomaterial for use in various medical applications. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9 KB 9 KB | Display Display | ![]() |
Images | ![]() | 223.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 216.1 KB | Display | ![]() |
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Full document | ![]() | 215.3 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Masked SV40 capsid, encapsulating DNA origami. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Simian virus 40
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Simian virus 40
Supramolecule | Name: Simian virus 40 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10633 / Sci species name: Simian virus 40 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host system | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 293 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta2) / Number images used: 7939 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Software - Name: RELION (ver. 3.0 beta 2) |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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